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Background  Aroma, berry firmness and berry shape are three main quality traits in table grape production, and also the important target traits in grapevine breeding. However, the information about their genetic mechanisms is limited, which results in low accuracy and efficiency of quality breeding in grapevine. Mapping and isolation of quantitative trait locus (QTLs) based on the construction of genetic linkage map is a powerful approach to decipher the genetic determinants of complex quantitative traits.    Results  In the present work, a final integrated map consisting of 3411 SLAF markers on 19 linkage groups (LGs) with an average distance of 0.98 cM between adjacent markers was generated using the specific length amplified fragment sequencing (SLAF-seq) technique. A total of 9 significant stable QTLs for Muscat flavor, berry firmness and berry shape were identified on two linkage groups among the hybrids analyzed over three consecutive years from 2016 to 2018. Notably, new stable QTLs for berry firmness and berry shape were found on LG 8 respectively for the first time. Based on biological function and expression profiles of candidate genes in the major QTL regions, 3 genes ( VIT_08s0007g00440 ,  VIT_08s0040g02740  and  VIT_08s0040g02350 ) related to berry firmness and 3 genes ( VIT_08s0032g01110 ,  VIT_08s0032g01150  and  VIT_08s0105g00200 ) linked to berry shape were highlighted. Overexpression of  VIT_08s0032g01110  in transgenic  Arabidopsis  plants caused the change of pod shape.    Conclusions  A new high-density genetic map with total 3411 markers was constructed with SLAF-seq technique, and thus enabled the detection of narrow interval QTLs for relevant traits in grapevine.  VIT_08s0007g00440 ,  VIT_08s0040g02740  and  VIT_08s0040g02350  were found to be related to berry firmness, while  VIT_08s0032g01110 ,  VIT_08s0032g01150  and  VIT_08s0105g00200  were linked to berry shape.

Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape